Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer dataset type classification start end gene chr ref_allele tum_allele1 tum_allele2 context MASP2 10747 broad.mit.edu 36 1 11020432 11020432 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 11020432 11020432 MASP2 1 C C G 26 FBXO42 54455 broad.mit.edu 36 1 16450213 16450213 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 16450213 16450213 FBXO42 1 C C A 28 AKR7A3 22977 broad.mit.edu 36 1 19483139 19483139 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19483139 19483139 AKR7A3 1 C C A 27 COL16A1 1307 broad.mit.edu 36 1 31890972 31890972 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31890972 31890972 COL16A1 1 C C A 26 SPOCD1 90853 broad.mit.edu 36 1 32053345 32053345 + Silent SNP G G T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 32053345 32053345 SPOCD1 1 G G T 41 SSBP3 23648 broad.mit.edu 36 1 54467080 54467080 + Missense_Mutation SNP A A T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54467080 54467080 SSBP3 1 A A T 8 INADL 10207 broad.mit.edu 36 1 62004545 62004545 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 62004545 62004545 INADL 1 C C T 21 FLG2 388698 broad.mit.edu 36 1 150593692 150593692 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150593692 150593692 FLG2 1 C C A 30 ATP8B2 57198 broad.mit.edu 36 1 152582580 152582580 + Missense_Mutation SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 152582580 152582580 ATP8B2 1 T T C 54 ARHGEF2 9181 broad.mit.edu 36 1 154188380 154188380 + Missense_Mutation SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 154188380 154188380 ARHGEF2 1 T T C 52 NHLH1 4807 broad.mit.edu 36 1 158607168 158607168 + Missense_Mutation SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 158607168 158607168 NHLH1 1 T T C 51 SCYL3 57147 broad.mit.edu 36 1 168091670 168091670 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 168091670 168091670 SCYL3 1 C C G 21 PLD5 200150 broad.mit.edu 36 1 240319968 240319968 + Silent SNP T T G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 240319968 240319968 PLD5 1 T T G 55 OR2W3 343171 broad.mit.edu 36 1 246126017 246126017 + Missense_Mutation SNP G G A rs12083024 byFrequency;byHapMap TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 246126017 246126017 OR2W3 1 G G A 48 PIK3AP1 118788 broad.mit.edu 36 10 98370188 98370188 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 98370188 98370188 PIK3AP1 10 C C T 22 AHNAK 79026 broad.mit.edu 36 11 62050498 62050498 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 62050498 62050498 AHNAK 11 G G A 47 MRPL49 740 broad.mit.edu 36 11 64649815 64649815 + Silent SNP G G T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 64649815 64649815 MRPL49 11 G G T 47 C2CD3 26005 broad.mit.edu 36 11 73511754 73511754 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73511754 73511754 C2CD3 11 A A G 6 FAT3 120114 broad.mit.edu 36 11 92216961 92216961 + Missense_Mutation SNP A A T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 92216961 92216961 FAT3 11 A A T 3 TMPRSS4 56649 broad.mit.edu 36 11 117483781 117483781 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 117483781 117483781 TMPRSS4 11 C C T 31 TECTA 7007 broad.mit.edu 36 11 120536216 120536216 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 120536216 120536216 TECTA 11 G G T 36 SLC38A4 55089 broad.mit.edu 36 12 45456983 45456983 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45456983 45456983 SLC38A4 12 G G A 42 MLL2 8085 broad.mit.edu 36 12 47723920 47723920 + Nonsense_Mutation SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 47723920 47723920 MLL2 12 G G A 46 SCN8A 6334 broad.mit.edu 36 12 50487199 50487199 + Missense_Mutation SNP A A T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50487199 50487199 SCN8A 12 A A T 2 ACVR1B 91 broad.mit.edu 36 12 50664218 50664218 + Splice_Site_SNP SNP G G C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Splice_Site_SNP SNP 50664218 50664218 ACVR1B 12 G G C 44 NCKAP1L 3071 broad.mit.edu 36 12 53197611 53197611 + Missense_Mutation SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53197611 53197611 NCKAP1L 12 T T C 56 NACA 4666 broad.mit.edu 36 12 55398181 55398181 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55398181 55398181 NACA 12 G G A 41 XPOT 11260 broad.mit.edu 36 12 63100528 63100528 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63100528 63100528 XPOT 12 G G C 48 GOLGA3 2802 broad.mit.edu 36 12 131875697 131875697 + Missense_Mutation SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 131875697 131875697 GOLGA3 12 T T C 60 ELF1 1997 broad.mit.edu 36 13 40415221 40415221 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 40415221 40415221 ELF1 13 G G C 41 OXGR1 27199 broad.mit.edu 36 13 96437140 96437141 + Missense_Mutation DNP GC GC AA novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 96437140 96437141 OXGR1 13 GC GC AA 34 EDDM3B 64184 broad.mit.edu 36 14 20308225 20308225 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20308225 20308225 EDDM3B 14 A A G 5 SLC39A2 29986 broad.mit.edu 36 14 20539252 20539252 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20539252 20539252 SLC39A2 14 C C T 29 MLH3 27030 broad.mit.edu 36 14 74584640 74584640 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74584640 74584640 MLH3 14 A A G 9 CACNA1H 8912 broad.mit.edu 36 16 1190530 1190530 + Silent SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 1190530 1190530 CACNA1H 16 C C T 29 FBXO39 162517 broad.mit.edu 36 17 6624415 6624415 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6624415 6624415 FBXO39 17 C C A 18 SLC47A2 146802 broad.mit.edu 36 17 19550635 19550635 + Silent SNP G G T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 19550635 19550635 SLC47A2 17 G G T 42 FAM134C 162427 broad.mit.edu 36 17 37990759 37990759 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37990759 37990759 FAM134C 17 C C T 30 WNK4 65266 broad.mit.edu 36 17 38202086 38202086 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 38202086 38202086 WNK4 17 C C G 25 HDAC5 10014 broad.mit.edu 36 17 39520443 39520443 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 39520443 39520443 HDAC5 17 G G C 48 COIL 8161 broad.mit.edu 36 17 52374485 52374485 + Splice_Site_SNP SNP T T A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 52374485 52374485 COIL 17 T T A 55 LAMA1 284217 broad.mit.edu 36 18 7023075 7023075 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7023075 7023075 LAMA1 18 C C A 30 LAMA3 3909 broad.mit.edu 36 18 19692763 19692763 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19692763 19692763 LAMA3 18 G G A 48 MALT1 10892 broad.mit.edu 36 18 54565850 54565850 + Silent SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 54565850 54565850 MALT1 18 C C T 30 INSR 3643 broad.mit.edu 36 19 7068323 7068323 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 7068323 7068323 INSR 19 A A G 1 GADD45GIP1 90480 broad.mit.edu 36 19 12926202 12926202 + Silent SNP G G C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 12926202 12926202 GADD45GIP1 19 G G C 41 EPS15L1 58513 broad.mit.edu 36 19 16389758 16389758 + Splice_Site_SNP SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 16389758 16389758 EPS15L1 19 C C A 18 CPAMD8 27151 broad.mit.edu 36 19 16952496 16952496 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 C A C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 16952496 16952496 CPAMD8 19 C C A 18 ZNF99 7652 broad.mit.edu 36 19 22733086 22733086 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22733086 22733086 ZNF99 19 C C A 28 RYR1 6261 broad.mit.edu 36 19 43707977 43707977 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43707977 43707977 RYR1 19 G G A 38 APOB 338 broad.mit.edu 36 2 21079652 21079652 + Missense_Mutation SNP A A T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21079652 21079652 APOB 2 A A T 8 MTIF2 4528 broad.mit.edu 36 2 55327035 55327035 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55327035 55327035 MTIF2 2 C C A 32 EIF2AK3 9451 broad.mit.edu 36 2 88671555 88671555 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 88671555 88671555 EIF2AK3 2 C C G 32 GCC2 9648 broad.mit.edu 36 2 108454151 108454151 + Missense_Mutation SNP T T G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 108454151 108454151 GCC2 2 T T G 57 IL1F9 56300 broad.mit.edu 36 2 113458926 113458926 + Silent SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 113458926 113458926 IL1F9 2 C C A 23 MBD5 55777 broad.mit.edu 36 2 148963614 148963614 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 148963614 148963614 MBD5 2 G G T 45 PIKFYVE 200576 broad.mit.edu 36 2 208908841 208908841 + Nonsense_Mutation SNP A A T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 208908841 208908841 PIKFYVE 2 A A T 1 SPHKAP 80309 broad.mit.edu 36 2 228589653 228589653 + Silent SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 228589653 228589653 SPHKAP 2 C C T 29 DTD1 92675 broad.mit.edu 36 20 18524815 18524815 + Silent SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 18524815 18524815 DTD1 20 G G A 34 ZNF341 84905 broad.mit.edu 36 20 31835302 31835302 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31835302 31835302 ZNF341 20 A A G 16 RBM12 10137 broad.mit.edu 36 20 33705596 33705596 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33705596 33705596 RBM12 20 C C T 32 HNF4A 3172 broad.mit.edu 36 20 42490438 42490438 + Silent SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 42490438 42490438 HNF4A 20 G G A 45 PREX1 57580 broad.mit.edu 36 20 46758287 46758287 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46758287 46758287 PREX1 20 C C A 25 RSPH1 89765 broad.mit.edu 36 21 42766027 42766027 + Silent SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 42766027 42766027 RSPH1 21 T T C 56 TRIOBP 11078 broad.mit.edu 36 22 36450946 36450946 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 36450946 36450946 TRIOBP 22 G G A 41 GRM7 2917 broad.mit.edu 36 3 7431806 7431806 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7431806 7431806 GRM7 3 C C T 19 FGD5 152273 broad.mit.edu 36 3 14837164 14837164 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 14837164 14837164 FGD5 3 G G C 43 MYH15 22989 broad.mit.edu 36 3 109595630 109595630 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 109595630 109595630 MYH15 3 C C T 28 PARP15 165631 broad.mit.edu 36 3 123836714 123836714 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 123836714 123836714 PARP15 3 G G A 36 PARP14 54625 broad.mit.edu 36 3 123905422 123905422 + Silent SNP A A T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 123905422 123905422 PARP14 3 A A T 7 RPN1 6184 broad.mit.edu 36 3 129827101 129827101 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129827101 129827101 RPN1 3 A A G 12 KIAA0232 9778 broad.mit.edu 36 4 6913893 6913893 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6913893 6913893 KIAA0232 4 G G T 34 HERC5 51191 broad.mit.edu 36 4 89644476 89644476 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89644476 89644476 HERC5 4 C C T 31 MAML3 55534 broad.mit.edu 36 4 141030778 141030778 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 141030778 141030778 MAML3 4 G G C 47 PLCXD3 345557 broad.mit.edu 36 5 41417998 41417998 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 41417998 41417998 PLCXD3 5 C C T 21 NSA2 10412 broad.mit.edu 36 5 74102274 74102274 + Silent SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 74102274 74102274 NSA2 5 T T C 61 POLK 51426 broad.mit.edu 36 5 74900959 74900959 + Silent SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 74900959 74900959 POLK 5 T T C 52 GABRA6 2559 broad.mit.edu 36 5 161049887 161049887 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 161049887 161049887 GABRA6 5 A A G 7 ODZ2 57451 broad.mit.edu 36 5 167607395 167607395 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 167607395 167607395 ODZ2 5 C C G 17 PANK3 79646 broad.mit.edu 36 5 167923585 167923585 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 167923585 167923585 PANK3 5 C C G 24 MSH5 4439 broad.mit.edu 36 6 31835702 31835702 + Silent SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 31835702 31835702 MSH5 6 A A G 3 ITPR3 3710 broad.mit.edu 36 6 33756419 33756419 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 33756419 33756419 ITPR3 6 A A G 2 HTR1E 3354 broad.mit.edu 36 6 87781917 87781917 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 87781917 87781917 HTR1E 6 C C A 18 PDE10A 10846 broad.mit.edu 36 6 165747019 165747019 + Missense_Mutation SNP A A C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 A C A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 165747019 165747019 PDE10A 6 A A C 8 INTS1 26173 broad.mit.edu 36 7 1506409 1506409 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1506409 1506409 INTS1 7 C C A 29 PSMA2 5683 broad.mit.edu 36 7 42930912 42930912 + Silent SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 42930912 42930912 PSMA2 7 C C T 25 URGCP 55665 broad.mit.edu 36 7 43884411 43884411 + Silent SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 43884411 43884411 URGCP 7 C C T 30 RABGEF1 27342 broad.mit.edu 36 7 65907680 65907680 + Silent SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 65907680 65907680 RABGEF1 7 T T C 51 RP1L1 94137 broad.mit.edu 36 8 10503593 10503593 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10503593 10503593 RP1L1 8 C C T 21 IDO2 169355 broad.mit.edu 36 8 39925913 39925913 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 39925913 39925913 IDO2 8 G G T 36 PXDNL 137902 broad.mit.edu 36 8 52483360 52483360 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52483360 52483360 PXDNL 8 A A G 11 ASAP1 50807 broad.mit.edu 36 8 131197069 131197069 + Missense_Mutation SNP T T C novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 131197069 131197069 ASAP1 8 T T C 50 PHF2 5253 broad.mit.edu 36 9 95456662 95456662 + Silent SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 95456662 95456662 PHF2 9 C C T 22 PHF8 23133 broad.mit.edu 36 X 54028157 54028157 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54028157 54028157 PHF8 23 C C G 30 TRO 7216 broad.mit.edu 36 X 54966870 54966870 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54966870 54966870 TRO 23 C C A 32 BEX2 84707 broad.mit.edu 36 X 102451537 102451537 + Silent SNP C C T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 102451537 102451537 BEX2 23 C C T 19 DUSP9 1852 broad.mit.edu 36 X 152568794 152568794 + Missense_Mutation SNP A A T novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 152568794 152568794 DUSP9 23 A A T 2 TP53 7157 broad.mit.edu 36 17 7518263 7518263 + Missense_Mutation SNP C C T rs11540652 byHapMap TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Missense_Mutation SNP 7518263 7518263 TP53 17 C C T 23 SRRM2 23524 broad.mit.edu 36 16 2753699 2753700 + Frame_Shift_Ins INS - TG - novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 2753699 2753700 SRRM2 16 - TG - 20 PTPRZ1 5803 broad.mit.edu 36 7 121466124 121466124 + Frame_Shift_Del DEL G - G novel Unknown TCGA-24-0979-01 TCGA-24-0979-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 121466124 121466124 PTPRZ1 7 G - G 47